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The Hidden Connection: How Pesticides in Our Food May Trigger Autoimmune Conditions

Pesticides free, Fresh organic vegetables including cabbage, daikon radish, potatoes, butternut squash, mushrooms, and bell pepper in a cardboard box on a rustic wood table, representing pesticide-free whole foods for autoimmune health.

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In my years of clinical practice, I’ve witnessed a troubling trend: autoimmune conditions are on the rise globally. Genetics were always to blame but I have been maintaining for years that our increasingly toxic environment is causative of this autoimmune explosion. Once such example of this what we eat. Our once lifegiving food supply has in most cases been replaced by chemical laden Frankenfoods due to the increasing prevalence of pesticide use. Pesticide residues on our food present an increasingly significant contributor to autoimmune processes in our bodies.

The Autoimmunity Epidemic

Autoimmune conditions now affect approximately 24% of Americans, with rates climbing steadily over the past decades. These conditions including rheumatoid arthritis, Hashimoto’s thyroiditis, multiple sclerosis, and inflammatory bowel disease are being normalized and we are all told that it’s just “genetic”. The reality is our bodies are trying desperately to sort out the increasing toxicity in our environment. The fact is, we are a beautifully designed and resilient so there will never be “one thing” that contributes to autoimmune processes in the body. Rather, it is a constellation of multiple toxicities, infections and environmental stressors that work in tandem to create a terrain becomes unhabitable. Pesticides have proven to be an increasingly hazardous threat to our immune systems and health and have been shown to be a major contributor to autoimmune processes.

Specific Autoimmune Conditions Linked to Pesticide Exposure

Don’t take my word for it, research has identified associations between pesticide exposure and numerous autoimmune conditions. While correlation doesn’t always equal causation, the growing body of evidence suggests these connections warrant serious attention:
  1. Rheumatoid Arthritis (RA): Multiple epidemiological studies have found associations between occupational pesticide exposure and increased RA risk. Agricultural workers exposed to certain insecticides show higher rates of rheumatoid factor, a key biomarker for this condition.
  2. Systemic Lupus Erythematosus (SLE): Research indicates connections between organochlorine pesticides and lupus development. These compounds have been found to induce autoantibody production similar to those seen in lupus patients.
  3. Multiple Sclerosis (MS): Geographic studies suggest correlations between agricultural pesticide use and MS incidence rates. Some research points to the role of pesticide-induced oxidative stress in myelin degradation.
  4. Hashimoto’s Thyroiditis: Organochlorine pesticides and other endocrine-disrupting compounds have been strongly implicated in thyroid autoimmunity. These chemicals can interfere with thyroid hormone production and trigger immune responses against thyroid tissue.
  5. Type 1 Diabetes: Several studies have found associations between prenatal and early-life pesticide exposure and development of type 1 diabetes, particularly with organophosphates disrupting pancreatic beta cell function.
  6. Inflammatory Bowel Disease (IBD): Both Crohn’s disease and ulcerative colitis have shown connections to pesticide exposure, largely through disruption of the gut microbiome and intestinal barrier function.
  7. Celiac Disease: Emerging research suggests environmental triggers including pesticides may contribute to celiac development in genetically susceptible individuals by altering intestinal permeability and immune function.
  8. Guillain-Barré Syndrome: Occupational exposure to organophosphate pesticides has been associated with increased risk of this neurological autoimmune condition.
  9. Sjögren’s Syndrome: Limited but growing evidence points to connections between pesticide exposure and this condition affecting moisture-producing glands.
  10. Psoriasis and Psoriatic Arthritis: Epidemiological studies have found correlations between pesticide exposure and increased incidence of these inflammatory skin and joint conditions.
Truthfully, we could keep going but the reality is almost all autoimmune conditions show there is a component of pesticide toxicity to them. While it is important to note that for most of these conditions, research shows associations rather than definitively established causal relationships, the truth is we don’t live in a vacuum and therefore research studies can never definitively say because in addition to pesticide exposure we are also exposed to massive amounts of electromagnetic radiation, thousands of other toxic chemicals daily on top of latent infections, nutrient deficiencies, and chronic life stressors. It is this constellation of environmental inputs with pesticides being a major contributor that leads to autoimmune disease.
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The Pesticide-Autoimmunity Connection

In an attempt to commercialize food production, modern agricultural practices have dramatically increased pesticide use on our food. While these chemicals are sold to control pests and prevent disease in the crops there is mounting evidence that shows that they not only harm the environment but also disrupt our body’s delicate immune balance through several mechanisms:

1. Intestinal Barrier Disruption

The gut lining serves as our first line of defense, carefully regulating what enters our bloodstream. Several studies have demonstrated that common pesticides can damage this protective barrier, creating intestinal permeability (often called “leaky gut”). When this barrier is compromised, partially digested food particles, toxins, and microbes can escape into the bloodstream, triggering immune responses. This process, over time, may confuse the immune system and lead to autoimmune reactions as the body begins producing antibodies against its own tissues. This is why any protocol or program to heal leaky gut has to include strict elimination of pesticides in the diet and environment.

2. Microbiome Disturbance

Our gut houses trillions of beneficial bacteria that play crucial roles in immune regulation. Recent research shows that pesticide residues can significantly alter this microbial ecosystem, reducing beneficial species like bifidobacterial while allowing harmful ones to flourish like clostridium and e.coli.

This dysbiosis creates inflammation and impairs the gut’s ability to regulate immune responses properly. Over time, this dysregulation may contribute to autoimmune development.

The probiotic industry in the United States generates $20 billion dollars a year as people search for answers to their dysbiosis and gut problems. Without cutting out pesticide containing foods the probiotics at best act as very poor brakes to the inevitable microbial destruction of the gut and ultimately autoimmune disoders.

3. Molecular Mimicry

Some pesticide compounds have molecular structures that resemble proteins in human tissues. Through a process called molecular mimicry, the immune system may develop antibodies against these pesticide compounds, which then cross-react with the body’s own tissues that share similar structural features.

An example of this phenomenon involves organophosphate pesticides and their structural similarity to myelin basic protein (MBP), a key component of the myelin sheaths around nerves that protects the nerve fibers. The phosphate-containing structures in these pesticides can trigger antibody production, and these antibodies may then cross-react with similar structures in MBP. This can contribute to demyelinating autoimmune conditions like multiple sclerosis, where the immune system attacks the myelin sheath.

Another documented example involves the pesticide chlorpyrifos used on fruit trees and corn, which can bind to proteins in the body, creating chlorpyrifos-protein adducts. These modified proteins may be recognized as foreign by the immune system, leading to antibody production. These antibodies can then cross-react with normal cellular proteins, particularly in neural tissue, contributing to neurological autoimmune conditions.

4. Endocrine Disruption

Many pesticides function as endocrine disruptors, interfering with hormone signaling throughout the body. Since hormones play critical roles in immune regulation, this disruption can promote autoimmune tendencies, particularly in thyroid conditions like Hashimoto’s.

As an example, pesticides like glyphosate can interfere with thyroid hormone production, conversion, and receptor binding. This disruption is particularly concerning because thyroid hormones regulate immune cell development and function. Studies show that individuals with elevated pesticide levels often have abnormal thyroid antibody profiles, suggesting a direct link to autoimmune thyroid conditions.

5. Direct Immune System Activation

Certain pesticides can directly stimulate immune cells, creating chronic low-grade inflammation. This persistent inflammatory state may eventually overwhelm the body’s regulatory mechanisms,  triggering autoimmune responses.

6. Critical Enzymatic Pathway Disruption

Dr. Stephanie Seneff, a Senior Research Scientist at MIT, has conducted extensive research on how certain pesticides particularly glyphosate (the active ingredient in Roundup) impact critical biochemical pathways. Her work highlights several concerning mechanisms that may connect pesticide exposure to autoimmunity:

Cytochrome P450 (CYP) Enzyme Inhibition: 

Dr. Seneff’s research suggests that glyphosate can inhibit cytochrome P450 enzymes, which are crucial for:
  • Detoxification of environmental chemicals
  • Activation of vitamin D
  • Metabolism of medications
  • Synthesis and breakdown of hormones
This inhibition creates a compounding effect where the body becomes increasingly unable to detoxify not only the glyphosate itself but also other environmental toxins, medications, and even naturally occurring compounds. As these substances accumulate, they may trigger or exacerbate autoimmune responses.

Shikimate Pathway Disruption:

While humans don’t possess the shikimate pathway (which is why glyphosate was initially considered safe for humans), Dr. Seneff points out that our gut microbiome does rely on this pathway. Her research suggests that:
  • Glyphosate selectively kills beneficial gut bacteria that depend on the shikimate pathway
  • This disrupts the production of critical amino acids like tryptophan and tyrosine
  • It also impairs the synthesis of folate and other essential nutrients
  • The resulting gut dysbiosis and nutritional deficiencies create conditions favorable for autoimmune development

Mineral Chelation Effects:

Dr. Seneff’s work also highlights glyphosate’s strong chelating properties as it was originally patented as a metal chelator before becoming an herbicide. This means it binds tightly to vital minerals, including:
  • Zinc (essential for immune function and over 300 enzymatic reactions)
  • Manganese (critical for mitochondrial function and antioxidant defense)
  • Cobalt (needed for vitamin B12 synthesis)
  • Copper (required for energy production and collagen formation)
  • Magnesium (involved in over 600 enzymatic reactions)
This chelation can effectively deplete the body of these minerals, creating deficiencies that compromise immune regulation and overall health. In autoimmune conditions, these mineral deficiencies can further impair the body’s ability to resolve inflammation and maintain proper tissue function.

Aluminum Synergy and Neurotoxicity:

Perhaps most concerning in Dr. Seneff’s findings is glyphosate’s interaction with aluminum, a widely prevalent environmental toxin. Her research proposes that:
  • Glyphosate forms complexes with aluminum, enhancing its absorption into the body
  • These aluminoglyphosate complexes can more easily cross the blood-brain barrier
  • Once in neural tissue, these complexes significantly increase aluminum’s neurotoxic effects
  • This may contribute to neurological autoimmune conditions like multiple sclerosis
The aluminum-glyphosate synergy is particularly troubling because aluminum is so prevalent in our environment from cookware and food packaging to medications, municipal water treatment and ambient air. This interaction effectively makes aluminum more bioavailable and potentially more harmful, especially for individuals with genetic predispositions to autoimmunity. Dr. Seneff has proposed that these disruptions may be particularly relevant in conditions like autism, celiac disease, and inflammatory bowel diseases, where both gut dysfunction and autoimmune components are present.

Clinical Findings: Pesticide Exposure Patterns in Autoimmune Patients

In my practice, I’ve observed distinct patterns when analyzing toxic burden testing in patients with autoimmune conditions:
  • Rheumatoid arthritis patients often show elevated organophosphate metabolites
  • Hashimoto’s thyroiditis cases frequently present with detectable levels of chlorinated pesticides
  • Multiple sclerosis patients commonly test positive for higher glyphosate levels
  • Inflammatory bowel disease sufferers regularly exhibit markers of multiple pesticide exposures alongside significant microbiome disruption
While individual cases vary significantly, these patterns align with research findings and suggest that addressing pesticide exposure should be part of a comprehensive treatment approach to autoimmunity.

The Most Problematic Pesticides

Not all pesticides appear to have equal effects on immune function. Research has identified several categories of particular concern:
  • Glyphosate: The active ingredient in Roundup herbicide is perhaps the most concerning based on Dr. Seneff’s research. Beyond its effects on the P450 and shikimate pathways mentioned above, studies suggest it may damage tight junctions in the intestinal lining and act as an antibiotic in the gut, selectively killing beneficial bacteria while allowing pathogens like Clostridium difficile to flourish.
  • Organophosphates: Among the most common agricultural pesticides, these have been linked to immune dysregulation and neurological impacts. They work by inhibiting acetylcholinesterase, an enzyme crucial for proper nervous system function, but research shows they may also disrupt immune cell signaling.
  • Neonicotinoids: This newer class of pesticides has immunomodulatory effects, with research suggesting they may alter T-cell and macrophage function—key components of the immune system involved in autoimmune regulation.
  • Chlorpyrifos: This insecticide has been linked to developmental issues and potential immune disruption. Research suggests it may alter cytokine production and T-cell function, potentially contributing to autoimmune dysregulation.
  • Atrazine: Commonly used on corn crops, atrazine has been shown to disrupt endocrine function creating hormone imbalances and alter immune responses, with particular concerns for thyroid function.
  • Organochlorines: Though many have been banned, these persistent compounds (including DDT) remain in the environment and continue to be detected in human tissues. They’ve been strongly associated with several autoimmune conditions, particularly lupus and rheumatoid arthritis.

1. Prioritize Organic When Possible

Organic certification prohibits the use of synthetic pesticides. While not everyone can afford to eat fully organic, focusing on the Environmental Working Group’s “Dirty Dozen” (foods with highest pesticide residues) can help you prioritize where to spend your organic food dollars.
It should also be noted that most grains (even organic) are sprayed with pesticides after they are harvested and therefore can maintain and “organic” certification. It is for this reason I do not recommend people consume and grain products (bread, pasta, crackers, etc.) while working on their healing.

2. Wash Produce Thoroughly

While washing won’t remove all pesticide residues (many are systemic within the plant), proper washing with water can reduce surface residues. For non-organic produce, soaking briefly in a solution of water with a small amount of baking soda can help remove additional residues.

3. Support Detoxification Pathways

The liver, kidneys, and digestive system work together to process and eliminate toxins. It is imperative to support proper drainage and detoxification of the organs of elimination. In the case of pesticides it is best to support these systems with:
  • Adequate hydration
  • Cruciferous vegetables (broccoli, cabbage, Brussels sprouts)
  • Antioxidant-rich foods (berries, leafy greens)
  • Sulfur-containing foods (garlic, onions)
To specifically support P450 enzyme function that Dr. Seneff highlights as critical, consider:

4. Replenish Minerals Chelated by Glyphosate

Based on Dr. Seneff’s research on glyphosate’s mineral-chelating properties, I recommend:

5. Minimize Aluminum Exposure

To counter the synergistic effects between glyphosate and aluminum it is important to:
  • Use aluminum-free cookware (cast iron, stainless steel, ceramic)
  • Choose aluminum-free personal care products (especially deodorants)
  • Filter drinking water to remove aluminum (distilled water is most effective)
  • Consume silica rich water frequently (Fiji, Volvic, Gerolsteiner)
  • Avoid aluminum-containing medications when alternatives exist
  • Be cautious with aluminum foil for cooking, especially with acidic foods

6. Heal the Gut

Once pesticide exposures have been minimized you can begin to focus on gut-healing nutrients like as intestinal barrier integrity is crucial for immune balance.
This should include:

5. Reduce Overall Toxic Burden

As discussed, pesticides are just one source of environmental toxins that can contribute to autoimmunity. It is important to reduce your overall exposure by:
  • Filtering drinking water
  • Using natural cleaning products
  • Choosing low-VOC household items
  • Avoiding plastic food containers
  • Using air purifiers in your home
  • Mitigating EMF exposure, especially in the bedroom while sleeping

The Path Forward

In order to overcome the overuse of pesticides and the ever increasing burden in our lives and on our bodies I believe we need to implement both an individual and collective approach to the pesticide issue.

Individual level: Take the steps outlined above to protect yourself and your family. Pay particular attention to eliminating sources of pesticides in your food supply and your home. Pay particular attention to your gut health utilizing both dietary and supplemental approaches.

Community level: Don’t settle for getting your produce at a large chain store. Talk to your local farms and support farmers who are transitioning to organic practices. Participate in community gardens and local groups advocating for cleaner food sources.

In my practice, I’ve seen remarkable improvements in autoimmune patients when we address environmental triggers like pesticide exposure and support the specific enzymatic pathways that pesticides compromise. While there’s still much to learn about these connections, the precautionary principle suggests we should minimize exposure while science catches up.

Your health journey is unique, and addressing pesticide exposure is just one piece of a comprehensive approach to autoimmunity. If you’re struggling with autoimmune symptoms, I encourage you book a complimentary call with us so we can learn more about your health journey and work to develop a personalized healing program that’s right for you.

*Disclaimer: This article is for informational purposes only and is not intended as medical advice. Always consult with a qualified healthcare provider before making changes to your diet, lifestyle, or treatment plans.

References

Pesticides and Autoimmunity – General
  1. Benbrook, C. M. (2016). Trends in glyphosate herbicide use in the United States and globally. Environmental Sciences Europe, 28(1), 3.
  2. Lerner, A., Jeremias, P., & Matthias, T. (2016). The world incidence and prevalence of autoimmune diseases is increasing. International Journal of Celiac Disease, 3(4), 151-155.
  3. Ford, E. S., Mannino, D. M., Wheaton, A. G., Giles, W. H., Presley-Cantrell, L., & Croft, J. B. (2014). Trends in the prevalence of obstructive and restrictive lung function among adults in the United States: findings from the National Health and Nutrition Examination surveys from 1988-1994 to 2007-2010. Chest, 145(5), 1043-1050.
  4. Mostafalou, S., & Abdollahi, M. (2017). Pesticides: an update of human exposure and toxicity. Archives of Toxicology, 91(2), 549-599.
Specific Autoimmune Conditions and Pesticide Exposure
  1. Parks, C. G., Walitt, B. T., Pettinger, M., Chen, J. C., de Roos, A. J., Hunt, J., Sarto, G., & Howard, B. V. (2011). Insecticide use and risk of rheumatoid arthritis and systemic lupus erythematosus in the Women’s Health Initiative Observational Study. Arthritis Care & Research, 63(2), 184-194.
  2. Corsini, E., Sokooti, M., Galli, C. L., Moretto, A., & Colosio, C. (2013). Pesticide induced immunotoxicity in humans: a comprehensive review of the existing evidence. Toxicology, 307, 123-135.
  3. Thrasher, J. D., Madison, R., & Broughton, A. (1993). Immunologic abnormalities in humans exposed to chlorpyrifos: preliminary observations. Archives of Environmental Health, 48(2), 89-93.
  4. Gold, L. S., Ward, M. H., Dosemeci, M., & De Roos, A. J. (2007). Systemic autoimmune disease mortality and occupational exposures. Arthritis & Rheumatism, 56(10), 3189-3201.
  5. Mandarapu, R., & Prakhya, B. M. (2015). In vitro myelotoxic effects of cypermethrin and glyphosate on human hematopoietic stem cells. Journal of immunotoxicology, 12(1), 37-45.
Dr. Seneff’s Research on Glyphosate
  1. Seneff, S., & Nigh, G. (2021). Toxic Legacy: How the Weedkiller Glyphosate Is Destroying Our Health and the Environment. Chelsea Green Publishing.
  2. Samsel, A., & Seneff, S. (2013). Glyphosate’s suppression of cytochrome P450 enzymes and amino acid biosynthesis by the gut microbiome: pathways to modern diseases. Entropy, 15(4), 1416-1463.
  3. Samsel, A., & Seneff, S. (2015). Glyphosate, pathways to modern diseases III: Manganese, neurological diseases, and associated pathologies. Surgical Neurology International, 6, 45.
  4. Seneff, S., Swanson, N., & Li, C. (2015). Aluminum and glyphosate can synergistically induce pineal gland pathology: connection to gut dysbiosis and neurological disease. Agricultural Sciences, 6(01), 42.
Intestinal Barrier Disruption and Microbiome Effects
  1. Shehata, A. A., Schrödl, W., Aldin, A. A., Hafez, H. M., & Krüger, M. (2013). The effect of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro. Current Microbiology, 66(4), 350-358.
  2. Aitbali, Y., Ba-M’hamed, S., Elhidar, N., Nafis, A., Soraa, N., & Bennis, M. (2018). Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice. Neurotoxicology and Teratology, 67, 44-49.
  3. Fasano, A. (2012). Leaky gut and autoimmune diseases. Clinical Reviews in Allergy & Immunology, 42(1), 71-78.
Mineral Chelation and Aluminum Interactions
  1. Krüger, M., Schledorn, P., Schrödl, W., Hoppe, H. W., Lutz, W., & Shehata, A. A. (2014). Detection of glyphosate residues in animals and humans. Journal of Environmental & Analytical Toxicology, 4(2), 1.
  2. Mesnage, R., & Antoniou, M. N. (2017). Facts and fallacies in the debate on glyphosate toxicity. Frontiers in Public Health, 5, 316.
  3. Exley, C. (2014). Why industry propaganda and political interference cannot disguise the inevitable role played by human exposure to aluminum in neurodegenerative diseases, including Alzheimer’s disease. Frontiers in Neurology, 5, 212.
Detoxification and Treatment Approaches
  1. Pizzorno, J. (2018). The Toxin Solution: How Hidden Poisons in the Air, Water, Food, and Products We Use Are Destroying Our Health–AND WHAT WE CAN DO TO FIX IT. HarperCollins.
  2. Lukiw, W. J. (2013). Alzheimer’s disease (AD) as a disorder of the plasma membrane. Frontiers in Physiology, 4, 24.
  3. Myers, A. (2015). The Autoimmune Solution: Prevent and Reverse the Full Spectrum of Inflammatory Symptoms and Diseases. HarperOne.
  4. Bland, J. S., Minich, D. M., Lerman, R. H., Darland, G., Lamb, J. J., Tripp, M., & Grayson, N. (2018). A systems medicine approach: Translating emerging science into individualized wellness. Advances in Medicine, 2018, 1-17.
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